DFT study of geometrical and vibrational features of small amino acids with polar side chains in hydrated media: L-Threonine and L-Serine

Geometry optimization at the B3LYP/6-31++G* level of calculation have been undertaken on clusters containing L-Threonine (L-Thr) or L-serine (L-Ser) surrounded by seven water molecules. This first step has been followed by the calculation of the harmonic vibrational modes. The comparison of the structural parameters of L-Thr and L-Ser with X-ray experimental values shows that the explicit model of solvation is more convenient. The discrepancies between the calculated values of bond lengths and bond angles with the experimental ones are less than 3%, excepted for OH, NtH, CβOH and CβCαH. The frequencies of the assigned modes are in good agreement with available IR and Raman values within 5%.